Variant report

Variant	rs11667254
Chromosome Location	chr19:36143494-36143495
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:36138960..36141162-chr19:36141370..36144327,2	K562	blood:
2	chr19:36139143..36141150-chr19:36143330..36145702,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000126267	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs170758	1.00[JPT][hapmap]
rs2311871	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4363955	0.87[ASN][1000 genomes]
rs4805137	0.87[ASN][1000 genomes]
rs4806189	0.87[ASN][1000 genomes]
rs61741212	0.87[ASN][1000 genomes]
rs67400004	0.87[ASN][1000 genomes]
rs7507525	0.80[YRI][hapmap]
rs9973289	0.89[CEU][hapmap];0.90[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv1060100	chr19:35658505-36170042	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv543993	chr19:35658505-36170042	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
4	nsv543995	chr19:36139204-36203592	Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11667254	UPK1A	cis	Esophagus Mucosa	GTEx
rs11667254	UPK1A	cis	normal skin	skin_eQTL
rs11667254	UPK1A-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs11667254	UPK1A	cis	Skin Sun Exposed Lower leg	GTEx
rs11667254	UPK1A	cis	lesional skin	skin_eQTL
rs11667254	UPK1A-AS1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36140000-36147800	Weak transcription	Aorta	Aorta
2	chr19:36140000-36148800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:36140000-36154000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr19:36140200-36152800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr19:36140400-36144800	Weak transcription	Brain Angular Gyrus	brain
6	chr19:36140400-36144800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr19:36140400-36144800	Weak transcription	Brain Germinal Matrix	brain
8	chr19:36140400-36144800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr19:36140400-36144800	Weak transcription	HMEC	breast
10	chr19:36140400-36144800	Weak transcription	HSMMtube	muscle
11	chr19:36140400-36144800	Weak transcription	NH-A	brain
12	chr19:36140400-36145000	Weak transcription	Brain Substantia Nigra	brain
13	chr19:36140400-36145200	Weak transcription	Fetal Kidney	kidney
14	chr19:36140400-36145400	Weak transcription	NHDF-Ad	bronchial
15	chr19:36140400-36146000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr19:36140400-36146600	Weak transcription	Fetal Brain Male	brain
17	chr19:36140400-36149200	Weak transcription	Small Intestine	intestine
18	chr19:36140400-36151600	Weak transcription	Stomach Mucosa	stomach
19	chr19:36140400-36164000	Weak transcription	Right Atrium	heart
20	chr19:36140600-36143800	Strong transcription	A549	lung
21	chr19:36140600-36144000	Strong transcription	Placenta	Placenta
22	chr19:36140600-36144800	Weak transcription	Hela-S3	cervix
23	chr19:36140600-36150400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr19:36140600-36153800	Strong transcription	Fetal Intestine Small	intestine
25	chr19:36140600-36157200	Strong transcription	Fetal Stomach	stomach
26	chr19:36140800-36143800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr19:36140800-36153800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr19:36141000-36143600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr19:36141000-36143600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr19:36141000-36143800	Strong transcription	H1 Cell Line	embryonic stem cell
31	chr19:36141000-36143800	Strong transcription	Fetal Intestine Large	intestine
32	chr19:36141000-36155600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr19:36141000-36157000	Strong transcription	Fetal Muscle Trunk	muscle
34	chr19:36141200-36143800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr19:36141200-36143800	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr19:36141200-36144800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr19:36141400-36143600	Strong transcription	Ovary	ovary
38	chr19:36141400-36143800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr19:36141400-36143800	Strong transcription	Adipose Nuclei	Adipose
40	chr19:36141400-36143800	Strong transcription	Liver	Liver
41	chr19:36141400-36143800	Strong transcription	Sigmoid Colon	Sigmoid Colon
42	chr19:36141400-36156800	Strong transcription	Spleen	Spleen
43	chr19:36141400-36157200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr19:36141600-36143600	Strong transcription	Colon Smooth Muscle	Colon
45	chr19:36141600-36143600	Strong transcription	HepG2	liver
46	chr19:36141600-36143800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr19:36141600-36143800	Strong transcription	Thymus	Thymus
48	chr19:36141600-36143800	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr19:36141600-36147000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr19:36141600-36151200	Strong transcription	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links